Starting phenix.real_space_refine on Sat Mar 16 01:04:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/03_2024/8tzj_41760_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/03_2024/8tzj_41760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/03_2024/8tzj_41760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/03_2024/8tzj_41760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/03_2024/8tzj_41760_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/03_2024/8tzj_41760_updated.pdb" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 4210 2.51 5 N 1184 2.21 5 O 1148 1.98 5 H 6772 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13346 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3494 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3495 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3151 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3150 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.04, per 1000 atoms: 0.45 Number of scatterers: 13346 At special positions: 0 Unit cell: (70.2, 83.16, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 26 16.00 P 4 15.00 Mg 2 11.99 O 1148 8.00 N 1184 7.00 C 4210 6.00 H 6772 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 4 sheets defined 60.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 50 through 58 removed outlier: 3.504A pdb=" N CYS A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 89 removed outlier: 3.851A pdb=" N ASN A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 179 through 195 removed outlier: 4.041A pdb=" N ARG A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'B' and resid 50 through 58 removed outlier: 3.504A pdb=" N CYS B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 removed outlier: 3.851A pdb=" N ASN B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 149 through 161 Processing helix chain 'B' and resid 179 through 195 removed outlier: 4.041A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'C' and resid 32 through 48 removed outlier: 4.331A pdb=" N TRP C 48 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 84 removed outlier: 3.739A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) Proline residue: C 68 - end of helix Processing helix chain 'C' and resid 188 through 228 removed outlier: 3.836A pdb=" N ALA C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 239 Processing helix chain 'C' and resid 243 through 286 Proline residue: C 249 - end of helix removed outlier: 4.135A pdb=" N GLY C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 282 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 324 removed outlier: 3.676A pdb=" N LEU C 302 " --> pdb=" O TRP C 298 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 49 removed outlier: 4.254A pdb=" N TRP D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 84 removed outlier: 3.870A pdb=" N LEU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR D 57 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 58 " --> pdb=" O ASN D 54 " (cutoff:3.500A) Proline residue: D 68 - end of helix Processing helix chain 'D' and resid 188 through 228 removed outlier: 3.509A pdb=" N ASP D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY D 219 " --> pdb=" O PHE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'D' and resid 243 through 287 Proline residue: D 249 - end of helix removed outlier: 4.049A pdb=" N GLY D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 326 removed outlier: 3.697A pdb=" N ALA D 316 " --> pdb=" O GLY D 312 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 90 through 93 removed outlier: 6.661A pdb=" N LEU A 167 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL A 93 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 169 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR A 198 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA A 170 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 200 " --> pdb=" O ALA A 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= D, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.661A pdb=" N LEU B 167 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL B 93 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 169 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR B 198 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA B 170 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 200 " --> pdb=" O ALA B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 355 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 10.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6766 1.03 - 1.23: 28 1.23 - 1.42: 2664 1.42 - 1.61: 3946 1.61 - 1.81: 52 Bond restraints: 13456 Sorted by residual: bond pdb=" C4 ADP B 302 " pdb=" C5 ADP B 302 " ideal model delta sigma weight residual 1.490 1.393 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C4 ADP A 302 " pdb=" C5 ADP A 302 " ideal model delta sigma weight residual 1.490 1.393 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C6 ADP B 302 " pdb=" N6 ADP B 302 " ideal model delta sigma weight residual 1.355 1.447 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C6 ADP A 302 " pdb=" N6 ADP A 302 " ideal model delta sigma weight residual 1.355 1.447 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C5 ADP B 302 " pdb=" C6 ADP B 302 " ideal model delta sigma weight residual 1.490 1.415 0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 13451 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.62: 269 106.62 - 113.59: 16057 113.59 - 120.56: 4824 120.56 - 127.53: 3165 127.53 - 134.50: 62 Bond angle restraints: 24377 Sorted by residual: angle pdb=" N LYS B 50 " pdb=" CA LYS B 50 " pdb=" C LYS B 50 " ideal model delta sigma weight residual 111.07 115.88 -4.81 1.07e+00 8.73e-01 2.02e+01 angle pdb=" N LYS A 50 " pdb=" CA LYS A 50 " pdb=" C LYS A 50 " ideal model delta sigma weight residual 111.07 115.85 -4.78 1.07e+00 8.73e-01 2.00e+01 angle pdb=" N GLN B 25 " pdb=" CA GLN B 25 " pdb=" C GLN B 25 " ideal model delta sigma weight residual 108.52 115.37 -6.85 1.63e+00 3.76e-01 1.76e+01 angle pdb=" N GLN A 25 " pdb=" CA GLN A 25 " pdb=" C GLN A 25 " ideal model delta sigma weight residual 108.52 115.34 -6.82 1.63e+00 3.76e-01 1.75e+01 angle pdb=" CA ALA A 48 " pdb=" C ALA A 48 " pdb=" N GLY A 49 " ideal model delta sigma weight residual 117.19 122.78 -5.59 1.50e+00 4.44e-01 1.39e+01 ... (remaining 24372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.57: 5969 26.57 - 53.14: 206 53.14 - 79.71: 35 79.71 - 106.28: 4 106.28 - 132.85: 2 Dihedral angle restraints: 6216 sinusoidal: 3431 harmonic: 2785 Sorted by residual: dihedral pdb=" O2A ADP A 302 " pdb=" O3A ADP A 302 " pdb=" PA ADP A 302 " pdb=" PB ADP A 302 " ideal model delta sinusoidal sigma weight residual -60.00 72.85 -132.85 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" O2A ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PA ADP B 302 " pdb=" PB ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 72.82 -132.82 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" O1B ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PB ADP B 302 " pdb=" PA ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 45.65 -105.66 1 2.00e+01 2.50e-03 3.05e+01 ... (remaining 6213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 920 0.051 - 0.103: 122 0.103 - 0.154: 26 0.154 - 0.206: 2 0.206 - 0.257: 4 Chirality restraints: 1074 Sorted by residual: chirality pdb=" C3' ADP A 302 " pdb=" C2' ADP A 302 " pdb=" C4' ADP A 302 " pdb=" O3' ADP A 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C3' ADP B 302 " pdb=" C2' ADP B 302 " pdb=" C4' ADP B 302 " pdb=" O3' ADP B 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C2' ADP B 302 " pdb=" C1' ADP B 302 " pdb=" C3' ADP B 302 " pdb=" O2' ADP B 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1071 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 18 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C LYS A 18 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS A 18 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 19 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 18 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C LYS B 18 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS B 18 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 19 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 44 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C GLY A 44 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY A 44 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS A 45 " -0.010 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 240 2.11 - 2.73: 24172 2.73 - 3.36: 36972 3.36 - 3.98: 44671 3.98 - 4.60: 72649 Nonbonded interactions: 178704 Sorted by model distance: nonbonded pdb=" HD1 HIS D 36 " pdb=" OH TYR D 252 " model vdw 1.490 1.850 nonbonded pdb=" HD1 HIS C 36 " pdb=" OH TYR C 252 " model vdw 1.537 1.850 nonbonded pdb=" HE2 PHE B 13 " pdb="HD11 LEU B 53 " model vdw 1.550 2.270 nonbonded pdb=" HE2 PHE A 13 " pdb="HD11 LEU A 53 " model vdw 1.551 2.270 nonbonded pdb=" O ALA D 284 " pdb=" H ASP D 288 " model vdw 1.639 1.850 ... (remaining 178699 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 9 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB or name OG or name H or name HA or name HB2 or name HB3)) \ or resid 52 through 228 or resid 301 through 302)) } ncs_group { reference = (chain 'C' and (resid 27 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ E1)) or resid 37 through 330)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 4.330 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 44.780 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 6684 Z= 0.286 Angle : 0.670 10.288 9050 Z= 0.341 Chirality : 0.040 0.257 1074 Planarity : 0.003 0.026 1130 Dihedral : 12.126 132.849 2450 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.15 % Allowed : 3.24 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.30), residues: 834 helix: 2.73 (0.23), residues: 508 sheet: -0.71 (0.77), residues: 56 loop : -0.67 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 48 HIS 0.002 0.001 HIS C 36 PHE 0.010 0.001 PHE C 32 TYR 0.008 0.001 TYR C 250 ARG 0.005 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8343 (mttt) cc_final: 0.8130 (mttm) REVERT: C 212 MET cc_start: 0.7410 (tpp) cc_final: 0.7209 (tpt) REVERT: C 302 LEU cc_start: 0.8034 (mt) cc_final: 0.7659 (tt) REVERT: D 76 LYS cc_start: 0.8437 (tttt) cc_final: 0.8229 (tptt) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.6889 time to fit residues: 134.5754 Evaluate side-chains 90 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6684 Z= 0.261 Angle : 0.580 6.422 9050 Z= 0.288 Chirality : 0.037 0.151 1074 Planarity : 0.003 0.033 1130 Dihedral : 8.489 123.263 940 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.74 % Allowed : 8.24 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.29), residues: 834 helix: 2.53 (0.22), residues: 514 sheet: -0.97 (0.73), residues: 66 loop : -0.47 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 256 HIS 0.021 0.002 HIS A 97 PHE 0.015 0.001 PHE C 215 TYR 0.012 0.001 TYR C 250 ARG 0.004 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8368 (mttt) cc_final: 0.8136 (mtmt) REVERT: B 39 MET cc_start: 0.8211 (ttt) cc_final: 0.8003 (ttp) REVERT: C 302 LEU cc_start: 0.8154 (mt) cc_final: 0.7910 (tt) REVERT: D 76 LYS cc_start: 0.8347 (tttt) cc_final: 0.8063 (tptt) REVERT: D 300 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7599 (mt-10) outliers start: 5 outliers final: 4 residues processed: 99 average time/residue: 0.5167 time to fit residues: 64.7174 Evaluate side-chains 94 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 81 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN B 221 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6684 Z= 0.221 Angle : 0.531 6.124 9050 Z= 0.260 Chirality : 0.036 0.148 1074 Planarity : 0.003 0.032 1130 Dihedral : 8.172 132.061 940 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.47 % Allowed : 8.82 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.30), residues: 834 helix: 2.57 (0.22), residues: 514 sheet: -0.96 (0.74), residues: 66 loop : -0.45 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.013 0.002 HIS A 97 PHE 0.011 0.001 PHE C 215 TYR 0.011 0.001 TYR C 250 ARG 0.003 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8308 (mttt) cc_final: 0.8102 (mtmt) REVERT: B 39 MET cc_start: 0.8314 (ttt) cc_final: 0.8076 (ttp) REVERT: C 302 LEU cc_start: 0.8035 (mt) cc_final: 0.7814 (tt) REVERT: D 76 LYS cc_start: 0.8271 (tttt) cc_final: 0.8044 (tptt) outliers start: 10 outliers final: 5 residues processed: 102 average time/residue: 0.5207 time to fit residues: 67.0230 Evaluate side-chains 94 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 208 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6684 Z= 0.230 Angle : 0.529 6.032 9050 Z= 0.259 Chirality : 0.036 0.148 1074 Planarity : 0.004 0.060 1130 Dihedral : 8.226 141.155 940 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.62 % Allowed : 9.41 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.30), residues: 834 helix: 2.58 (0.22), residues: 514 sheet: -1.09 (0.73), residues: 66 loop : -0.39 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.009 0.001 HIS A 97 PHE 0.012 0.001 PHE D 189 TYR 0.013 0.001 TYR C 250 ARG 0.008 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8303 (mttt) cc_final: 0.8091 (mtmt) REVERT: D 76 LYS cc_start: 0.8296 (tttt) cc_final: 0.8055 (tptt) outliers start: 11 outliers final: 7 residues processed: 102 average time/residue: 0.5342 time to fit residues: 67.9006 Evaluate side-chains 97 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6684 Z= 0.284 Angle : 0.554 6.070 9050 Z= 0.273 Chirality : 0.037 0.145 1074 Planarity : 0.004 0.052 1130 Dihedral : 8.448 153.959 940 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.76 % Allowed : 10.74 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.30), residues: 834 helix: 2.45 (0.22), residues: 522 sheet: -1.19 (0.73), residues: 66 loop : -0.37 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.009 0.001 HIS C 323 PHE 0.013 0.001 PHE C 215 TYR 0.013 0.001 TYR C 250 ARG 0.006 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8338 (mttt) cc_final: 0.8073 (mtmt) REVERT: D 76 LYS cc_start: 0.8333 (tttt) cc_final: 0.8088 (tptt) outliers start: 12 outliers final: 10 residues processed: 102 average time/residue: 0.5146 time to fit residues: 66.1794 Evaluate side-chains 101 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.0010 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6684 Z= 0.175 Angle : 0.518 6.269 9050 Z= 0.249 Chirality : 0.035 0.148 1074 Planarity : 0.003 0.041 1130 Dihedral : 8.390 159.100 940 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.32 % Allowed : 12.35 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.30), residues: 834 helix: 2.60 (0.22), residues: 522 sheet: -1.19 (0.72), residues: 66 loop : -0.25 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.007 0.001 HIS A 97 PHE 0.009 0.001 PHE C 215 TYR 0.010 0.001 TYR D 250 ARG 0.007 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8259 (mttt) cc_final: 0.8005 (mtmt) REVERT: D 76 LYS cc_start: 0.8318 (tttt) cc_final: 0.8064 (tptt) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.4891 time to fit residues: 62.8316 Evaluate side-chains 99 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 chunk 37 optimal weight: 0.0770 chunk 32 optimal weight: 0.4980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6684 Z= 0.154 Angle : 0.509 6.335 9050 Z= 0.245 Chirality : 0.035 0.145 1074 Planarity : 0.003 0.043 1130 Dihedral : 8.455 163.748 940 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.32 % Allowed : 12.50 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.31), residues: 834 helix: 2.71 (0.23), residues: 522 sheet: -1.15 (0.72), residues: 66 loop : -0.15 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.006 0.001 HIS A 97 PHE 0.011 0.001 PHE C 291 TYR 0.010 0.001 TYR C 250 ARG 0.006 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8225 (mttt) cc_final: 0.7983 (mtmt) REVERT: D 76 LYS cc_start: 0.8307 (tttt) cc_final: 0.8059 (tptt) outliers start: 9 outliers final: 7 residues processed: 101 average time/residue: 0.5231 time to fit residues: 67.7839 Evaluate side-chains 98 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6684 Z= 0.184 Angle : 0.514 6.299 9050 Z= 0.247 Chirality : 0.035 0.145 1074 Planarity : 0.003 0.058 1130 Dihedral : 8.811 175.885 940 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.32 % Allowed : 12.21 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.31), residues: 834 helix: 2.75 (0.23), residues: 522 sheet: -1.12 (0.73), residues: 66 loop : -0.07 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.005 0.001 HIS A 97 PHE 0.010 0.001 PHE C 291 TYR 0.010 0.001 TYR C 250 ARG 0.009 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8214 (mttt) cc_final: 0.7975 (mtmt) REVERT: D 76 LYS cc_start: 0.8315 (tttt) cc_final: 0.8082 (tptt) outliers start: 9 outliers final: 7 residues processed: 99 average time/residue: 0.5071 time to fit residues: 63.7238 Evaluate side-chains 97 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6684 Z= 0.196 Angle : 0.518 6.174 9050 Z= 0.249 Chirality : 0.035 0.145 1074 Planarity : 0.003 0.028 1130 Dihedral : 8.900 176.191 940 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.03 % Allowed : 12.50 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.31), residues: 834 helix: 2.79 (0.23), residues: 522 sheet: -1.11 (0.73), residues: 66 loop : -0.01 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.005 0.001 HIS A 97 PHE 0.009 0.001 PHE C 291 TYR 0.011 0.001 TYR D 250 ARG 0.005 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8207 (mttt) cc_final: 0.7953 (mtmt) REVERT: D 76 LYS cc_start: 0.8312 (tttt) cc_final: 0.8081 (tptt) outliers start: 7 outliers final: 7 residues processed: 99 average time/residue: 0.5019 time to fit residues: 62.8006 Evaluate side-chains 98 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6684 Z= 0.273 Angle : 0.556 6.087 9050 Z= 0.272 Chirality : 0.036 0.146 1074 Planarity : 0.004 0.068 1130 Dihedral : 8.953 179.681 940 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.32 % Allowed : 12.21 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.31), residues: 834 helix: 2.68 (0.23), residues: 522 sheet: -1.12 (0.73), residues: 66 loop : -0.10 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 298 HIS 0.005 0.001 HIS C 323 PHE 0.011 0.001 PHE C 215 TYR 0.013 0.001 TYR D 250 ARG 0.009 0.001 ARG A 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8262 (mttt) cc_final: 0.8002 (mtmt) REVERT: B 104 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8094 (t) REVERT: D 76 LYS cc_start: 0.8369 (tttt) cc_final: 0.8133 (tptt) outliers start: 9 outliers final: 6 residues processed: 99 average time/residue: 0.5058 time to fit residues: 63.5027 Evaluate side-chains 98 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 0.0000 chunk 27 optimal weight: 0.0050 chunk 68 optimal weight: 0.8980 chunk 8 optimal weight: 0.0060 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105191 restraints weight = 27879.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109674 restraints weight = 14131.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112591 restraints weight = 8826.114| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6684 Z= 0.141 Angle : 0.504 6.334 9050 Z= 0.241 Chirality : 0.035 0.145 1074 Planarity : 0.003 0.054 1130 Dihedral : 8.797 179.765 940 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.44 % Allowed : 13.38 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.31), residues: 834 helix: 2.90 (0.23), residues: 522 sheet: -1.03 (0.74), residues: 66 loop : 0.04 (0.43), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 298 HIS 0.005 0.001 HIS A 97 PHE 0.008 0.001 PHE C 32 TYR 0.009 0.001 TYR C 250 ARG 0.007 0.000 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3165.95 seconds wall clock time: 56 minutes 13.59 seconds (3373.59 seconds total)